Oncology Tissue Services

A service center of JHU

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Analysis Software

Analysis Tools

One of the major benefits of digitizing histologic glass slides is to perform quantitative analysis of staining features. Analysis tools can be used to identify percent areas of fibrosis, percent areas of necrosis, percent of cells stained with a particular antibody, intensity of staining with a particular antibody and many other uses. The TMA core facility now provides many tools to perform analysis on both tissue microarrays and whole slide images for users to explore on their own. The TMA core does not currently provide any fee for service analysis services. We will meet with investigators to consult at a fee for service to plan analysis projects. It is strongly recommended that investigators view the available tutorial materials provided on our website before requesting consultation.

Aperio Toolbox

The TMA Core facility has purchased portions of the Aperio Image Analysis Toolbox. These tools are free to use for all slides scanned through the TMA core facility. The tools are available through the Spectrum Server, by opening an image in ImageScope and selecting View -> Analysis. The available tools are membrane quantification, nuclear quantification, rare event detection and color deconvolution. The tools work with both whole slide images and tissue microarrays. Tutorials and documentation for these tools are available on the "Aperio Toolbox" page.


FrIDA is an analysis tool built by Jim Morgan and Toby Cornish to be used with tissue microarrays analyzed through TMAJ. It has some sophisticated filtering features not available through the Aperio Toolbox. There is a less sophisticated version of FrIDA that is available for use with .jpg or .tif images capture from a whole slide image. However, that is no longer recommended. FrIDA is accessible through TMAJ by starting a new Image Analysis Session on the Scan ID folder of the images of interest.